Same Side by Yachi [PG-13]
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Summary: Atlantis is home, and the team has a whole new basket of apples to deal with: keeping the city hidden, staving off a Wraith invasion, power shortage and...oh yeah, the giant alien robots. Crossover with Transformers movieverse.

Categories: Crossovers > General
Characters: John Sheppard, Major Lorne, Other, Rodney McKay, Ronon Dex
Genres: Action/Adventure, Team
Warnings: None
Chapters: 26 [Table of Contents]
Series: None

Word count: 93237; Completed: Yes
Updated: 12 Dec 2009; Published: 14 Jul 2009

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Story Notes:
Now complete, this is a very, very long story about how Sheppard and his team must work with the NEST team to fight aliens. Lots and lots of aliens.

Author's Chapter Notes:
I have issues, apparently. This chapter won't contain much action, but you can see where it's going. Obviously, it contains spoilers for the Season 5 finale of Stargate: Atlantis, and probably most of the Transformers movies, as well. Enjoy!

                The sound of the ocean was a great thing to listen to in the morning. Sheppard made a habit of listening to it a few minutes before he got out of bed to start his day. Of course, back then in the Pegasus galaxy, the ocean was pretty much the only thing you heard in the morning: the sound of waves crashing into the piers of the ancient city and a gentle soothing breeze through the skyscraping towers. Nah, here he heard all that and the sounds of San Francisco just a mile away from his window: traffic, car horns, sirens, airplanes and all that.

                Staying in Atlantis had been his decision. It was extremely personal: Earth was great, sure, but Atlantis was still home. Who cared what planet it was on? Atlantis was Atlantis. Nothing much happened around here anymore, since most of the personnel moved back to the SGC or other Stargate program attachments. The 'Atlanteans' as everyone knew them fell apart and the city was manned by a handful of the diehard members of the original expedition, and a lot of new guys.

                Explaining how to use the strange Ancient toilets more than once was hard enough—getting used to the new Atlantis was not fun, sure, but Sheppard could take it.

                "John! John! I know you're not sleeping. I need you in the Gate Room—these incapable morons are driving me absolutely insane! Sheppard? Oh, come on, like I believe you're actually sleeping this time."

                Then there was McKay.

                Sheppard rolled out of his bed, already fully clothed in his expedition gear. Naptime was over. "Hey, Rodney," he said with mild conviction. "Nice of you to drop in."

                His scientist counterpart and team member-became-friend rolled his eyes, as if the entire world had gone crazy; then again, it kinda had. "Gate Room. Acting witty doesn't help me get the Playskool PhDs in line. You know what today is?"

                Of course the Lieutenant Colonel knew what day it was, but just to dryly humour him, he folded his arms and said, "No, Rodney. What day is it?"

                "Uh, only the biggest deadline in my career?. As in, two days after I assured Landry I'd have the Atlantis gate recalibrated to work in tandem with Earth's main Stargate, which is being removed from the SCG as we speak and put into classified storage space, meaning if I don't finish this—"




                Sheppard couldn't blame him for being completely stressed out. Whereas nothing interesting had happened since their arrival on Earth, the big stuff was still coming. 'Big', as in Stargate Command being relocated to Atlantis, and the city being moved to a remote island a few hundred clicks down the coast. After more than a decade of good old planetary defense, the SGC was getting a facelift and Atlantis was going to be the new 'temporary' headquarters for all off-world business until they finished remodeling the old hangar. A few months, maybe was something to look forward to, at least.

                He finally stood up, ignoring McKay's 'finally' look, and headed out into the familiar corridors of the city. By now, he could blindfold and hogtie himself, and he'd still make it to the Gate Room without even breaking a sweat. It made him feel proud, though left him wondering if he should consider a vacation. A little one.

                "Hey." Ronon's voice joined him, then Ronon himself as the tall Satedan fell into stride next to him. He always had this habit of showing up out of nowhere. "McKay wake you up, too?"

                "There you are!" McKay himself snapped before Sheppard could open his mouth. "Weren't you supposed to be ready hour ago?" he accused, glancing at his watch.

                "I got hungry," came the nonchalant reply.

                "Rodney, could you tell us what exactly it is you want us for? It's seven A.M. It's not even breakfast yet."

                That earned him a sharp glare. Again, bad Sheppard: he shouldn't ever question the issues of the chief scientific advisor of the city of Atlantis. McKay launched into a halting explanation. "Okay, problem one: Atlantis' Stargate is  a little more modern in design than the SGC gate, and overriding the interface between Earth's galactic positioning grid and the Ancients' version of a G.P.S. is—"

                "Next problem," pressed the colonel.

                "We can dial out," McKay finished in a hurry, sounding very unsure of himself. The trio slowed to a stop, as John turned a long, penetrating look on the scientist.

                "Why do I get this feeling like that's not a good thing?"

                McKay winced, just barely. "Well, we should be able to dial out. Problem is, we were only sent a partial download of the S.G.C. database, and I mean partial. We've only got about six local addresses to choose as a test site within the projected 'safe wormhole' quadrant and...well, none of them are exactly Alpha...worthy."

                After a lengthy moment, Sheppard tilted his head towards him. "Rodney, we've had this discussion before. Me and Ronon aren't guinea pigs."

                "Seriously, colonel?" Though it hardly seemed possibly, McKay sounded even more annoyed by that. "Would I even consider sending you through a wormhole I wasn't a hundred percent sure was stable? Or to a planet I suspected was deadly? Besides...I, uh...I'm coming, too."

                Ronon looked at the colonel, and the colonel looked back at him with a slight smirk. "It's safe," the Satedan concluded, before setting off down the corridor.

                "Yep." Sheppard followed him, now grinning broadly.

                "Oh, very funny." And third as usual, the astrophysicist jogged behind them in an effort to keep up.

                McKay wasn't kidding. The Gate Room was packed with people, dozens of unfamiliar faces doing strange things and totally ignoring the trio of Sheppard's team. In retrospect, there were always weird people swarming the Stargate these days. And there was a lot more military presence than usual. Sheppard spotted lots of army uniforms, where he'd normally see Atlantis uniforms—exactly what he liked to see, hard-working men and women of the Army, Marines, and Air Force all working together. This was kind of like military domination, and he didn't like it just because he happened to be an Air Force Lieutenant Colonel, but because they were doing his job for him. Heck, he didn't even know what that job was right now.

                If only Teyla stayed on Atlantis. She and Kanaan found an apartment in San Francisco...actually, he didn't know what she was doing. She'd been acting strangely since they came back to Earth a few months past and stayed pretty much out of touch. Sometimes he heard things from Rodney, who heard things from Keller, but that was the closest thing he had to contact with her.

                To his surprise, he soon spotted General Landry briskly walking their way, in a way that suggested he had something important to share. Not that he knew him personally, but Landry struck him as the kind of guy who didn't jump all over the place in difficult situations. Sheppard recognized the professional vibe in the air and gave him a quick salute, just out of polite formality. The general returned it and nodded to his team.

                "Sorry to be the bearer of bad news, Colonel," he started with a passively furled brow. "There won't be any off-world exploration today; in fact, Stargate travel has been suspended until oh six hundred hours tomorrow morning. They're sending me to Washington for an emergency debriefing, and I'm requesting your team to be SGC's official representative."

                Sheppard shot a side-long glance at Rodney, who looked just as baffled as he felt. He had a bad feeling about this. "With all due respect, sir, Washington is the reason we're still on Atlantis. If this is about reassignment---"

                "Don't worry about that, Colonel," Landry assured him, side-stepping to allow a group of four scientists carrying something covered under a white cloth to pass by. "I'm not at liberty to tell you what this is about, but these are orders are directly from Admiral Warner from Homeworld Security."

                He had to pause before asking, because Sheppard was the kind of guy who had to make sure of things before jumping to conclusions. "You whole team to go to Washington, you mean."

                "Actually, Georgia. With the exception of Teyla, who already turned down the formal request for maternal reasons. Same goes to you, Ronon, since you're considered an ally out of our jurisdiction. You've been given the same level of clearance, should you choose to accept it."

                "Where Sheppard goes, I go," the Satedan responded simply, as though it were as simple as that. "So what kind of clearance?"

                "You'll find out when you arrive in Quantico." Landry sighed, turning around to face Atlantis' Stargate. "That's where you'll be fully briefed on the situation and meet up with the other members of your team."

                "Whoa, whoa, hold on," McKay jumped in. "Quantico? As is, gigantic Marines base Quantico? That has to be like...the farthest thing from Washington, Cheyenne Mountain or Atlantis. It's a five hour flight! Not to mention I have a Stargate program to get back up and running, like...three hours ago yesterday."

                "Dr. Zelenka will be filling yours shoes while you're away, Dr. McKay." Over the years, even General Landry was getting used to, and learning how to deal with the astrophysicists difficult outbursts. "I assure you that what you'll be dealing with makes this business seem almost elementary in comparison." His eyes traveled to Sheppard with the all of the sharpness of a military general. "Six hundred hours tomorrow, Colonel. Now if you'll excuse me, I have to go pack that bag I just unpacked this morning..."

                Whatever was bigger than Atlantis, or the Stargate, or the Stargate Program for that matter, John was suddenly wishing he'd chosen to retire early when he got back. Heck, this time, he didn't even get the option—that's what happened when you knew too much about aliens and Earth invasions. He looked at his teammates. Ronon didn't seem fazed, as always; he wouldn't be surprised if the big guy was actually looking forward to the exciting stuff. Rodney on the other hand looked like someone had slapped him. In a way, someone kinda did. This was the 'big thing' McKay had been working on for the past few weeks, and to let a bunch of new people take over and finish the job (probably get the credit, too) was the equivalent to taking a P-90 and letting it rip all over the Mona Lisa...If Rodney had been an art fan. Maybe his analogies needed work.

                And he was just getting used to the idea of sleeping in.

                Two trashed Decepticon bodies. Sixteen minutes of all-out melee, deafening explosions, propelled rockets, blood and whatever passed for robot blood, and collective sweat. Divide one with the other, and you got eight dead men.

                That meant eight flags, eight caskets, and eight lies to cover up the reason each and every man died on the hot and humid plains of Northeast Florida outside a military outpost with unbreakable security clearance. Deceptions needed Energon, and the Autobots happened to have a small cache stored there while investigating a strange energy signal picked up by one of NORAD's satellites. The signal had been a decoy. The Decepticons didn't have the human resources that the Autobots had, and openly attacking and robbing power plants of their resources would draw too much attention. A trap. Whole damned thing had been a trap.

                Crankcase and Steamhammer were dead, of course: piles of scrap metal in the middle of a scorched battlefield littered with the remains of two tanks. Two halves of the first tank to be ripped apart lay sprawled, like red-hot molten skeletons no less than fifteen yards apart. The two soldiers inside weren't as lucky. It would probably take hours to try and collect their remains.

                In the smokescreen of the aftermath, a much-battered Optimus Prime, Ironhide and Ratchet stood on the battlefield as the wounded and dead were carted away. There were vehicles surrounding the dead Deceptions and prepping their removal at twice the speed of everyone else. Lennox didn't realize he was staring at them until he noticed Optimus' looming presence next to him.

                "Megatron is growing desperate indeed," the leader of the Autobots said gravely. "I am sorry, Major Lennox. We did not foresee an attempt on our supplies of Energon, as all Cybertronians know how unwise open battle is so near even the smallest of supplies."

                "Yeah," the major replied without much conviction. "Well, like you said—this isn't like Megatron. So either Starscream is starting to act out, or we've rogue Decepticons all over again. I don't know which is worse."

                Optimus shook his head. "Neither. Both scenarios spell disaster, for both Autobots and humankind. For now, we will remove our stores of Energon from your custody and hide them in a remote location, in order to prevent your military from suffering any more in our name."

                Lennox craned his head to look up at the Autobot with an undefined expression. "Somehow I'm feeling the need to remind you, big guy, that you're the ones defending the whole planet from these maniacs. Keeping an eye on your fuel source? That's nothing. Request for transport of military good denied."

                The equivalent of a sigh was his first indication that he'd said something half-wrong. Or half-right. "The danger placed upon human lives cannot go overlooked."

                "Never thought I'd say this, Optimus," Lennox replied, turning around. He gave the Autobot a companionable clout on his leg as he began to head for the base. "For once, think about your own life. You need that Energon, and we won't risk losing it because it's not under our protection. Go see Ratchet, get fixed up, and we'll talk about it later."

                Other than the fact that he'd just given the immensely powerful leader of the Autobots the brush-off, Lennox was feeling like nothing could make his day worse. A hot shower and a big lunch might make it better, though. He could feel the sharp sting of the shrapnel cuts on his face and his leg was sore from landing on it wrong. He was dirty as hell and tired, too. He'd known one of the soldiers who died inside what was left of the tank—Sergeant Underhill, an ex-boxer with twin baby boys at home. He'd lost to his triple ace three-of-a-kind four nights ago. Wouldn't be the last time he had to see a good man go down, but it didn't make it any better to start thinking that way.

                The jeep that pulled up alongside him didn't even catch his attention until he saw a man get out and start to walk his way. Lennox considered breaking for it, fake an emergency call over his radio or pretend he had to piss really bad, but he didn't have the energy. The suited official either was too blue to notice the carnage on the field just outside of the base, or it didn't bother him. Before he knew it, Lennox was looking at a tanned face with dark shades. Quaint security disguise—he wondered if this guy was Secret Service, or an overreaching CIA agent. Maybe neither.

                "Major Lennox. Special Interests Agent Palmer of the Department of Homeland Security. I won't waste your time, considering the state of things," the man started, holding out a folder and flashing his credentials at the same time. Lennox stared at him for a moment, before reaching out with a muddy hand to take it. "These are orders directly from the Secretary of Defense. Be assured that the contents are unrelated to the events that unfolded today. I've been told to tell you that this is an emergency requisition of your time and resources, and requires your attention to another branch of classified material under Executive Order 13292."

                Well, Lennox wasn't used to getting his orders from anyone outside of the United States Army, or members of the cabinet themselves where concerning global emergencies...and he'd never heard of a 'Special Interest Agent' in any operating government agency. He held onto the sealed folder and narrowed his eyes at the 'agent'. "Thanks," was all he said.

                Agent Palmer tilted his head at him slightly, glanced over his shoulder at the grouped Autobots standing a few dozen meters past the major's shoulder, then got back into the jeep. Unfazed. Lennox watched the taillights of the vehicle a moment before looking down at the folder in his hands. It had 'Top Secret' in bold, almost cheesy letter across the front. Just like in the days when he'd first learned everything he knew about the Autobots.

                He tore open the seal to take a look at the letter of introduction, written by Secretary Keller himself. When the paragraph sunk in, the first thing he began to wonder was how he would tell Optimus and the others that they wouldn't be rejoining the other Autobots back in Diego Garcia.